Since no answer suggests the exact option combination that I use, here it is:
git clean -dfx
git checkout .
This is the online help text for the used git clean options:
-d
Remove untracked directories in addition to untracked files. If an untracked directory is managed by a different Git repository, it is not removed by default. Use -f option twice if you really want to remove such a directory.
-f
If the Git configuration variable clean.requireForce is not set to false, Git clean will refuse to delete files or directories unless given -f, -n, or -i. Git will refuse to delete directories within the .git subdirectory or file, unless a second -f is given.
-x
Don’t use the ignore rules from .gitignore (per directory) and $GIT_DIR/info/exclude, but do still use the ignore rules given with -e options. This allows removing all untracked files, including build products. This can be used (possibly in conjunction with git reset) to create a pristine working directory to test a clean build.
Also, git checkout . needs to be done in the root of the repo.